We propose to commercialize a high-sensitivity, low-cost fluorescence- based DNA fragment analyzer with at least ten times higher throughput than current instruments. Such an instrument is essential to accelerating our understanding of cancer and other heritable diseases by making it cost-effective to perform large-scale genetic linkage analysis employing thousands of genetic markers. In Phase l we will construct the prototype fragment analyzer and demonstrate its ability to separate and automatically size fluorescently-labeled polymerase chain reaction products at detection limits approaching 20 attomoles per band. This will involve 1) construction of the prototype scanning fluorescence detector, 2) the codevelopment of fluorescently labeled genetic markers and size standards with Dr. James Weber's laboratory at Marshfield Medical Research Foundation, 3) the determination of detection limits for the fluorophores that will be used in labeling the genetic markers and size standards, 4) the evaluation of electrophoresis buffers and their effect on gel reusability, and 5) the development and refinement of genotyping software. In Phase 2 we will improve the throughput and refine the operating and analysis software. This will be accomplished in collaboration with Dr. Weber as he pursues the creation of a genotyping factory at Marshfield. PROPOSED COMMERCIAL APPLICATION: This next-generation DNA fragment analyzer will be far more cost-effective, require smaller amounts of dye-labeled DNA, and achieve throughputs of at least an order of magnitude higher than current automated instruments. This machine will make it practical to study entire populations, each with over one hundred markers, in order to discover, detect, diagnose and track a wide variety of genetic diseases.